Hi Falcon-
Hey, you and the Dalai Lama! His stomach and your shoulders. You are in good company. I would be extremely surprized if he decides to stop meditating.
#1 - the exercises don't cause something like this. I think it was already there. I had a few random thoughts.. Arthritis does come in cycles, out of nowhere, can be very painful, then disappear. It does effect the muscles and tendons in the same area. Now, lets go back to thinking of it as a nameless blockage. In my opinion, you should really try to focus on relaxing and opening up. Really get into the moving of yin and yang, bringing focused energy to areas you speak of. You have a strong name you have chosen to use in this forum. Use some of that strength as focused intention, in conjunction with an increased level of relaxation and opening up.
Same for the breathing of the universe. Those two exercises shouldn't challenge the lifting of your arms, as your elbows are dropped. I sometimes experience this type of blockage. I work through it. I don't limit myself, I turn up the qigong work, and get back in balance. For me, it is sometimes triggered by coffee, and/or work related physical stress. If I do either, to a greater degree than my qigong work, I start to feel blockages. I might add here, that I was told that there is a school for qigong healers in China, where the requirement for entry, is being a self healed survivor of cancer. This is referring to a level of achievement in self concentration. By all means, if you feel you may have something that you would feel should be looked at by a physician, check it out...but, don't stop your qigong work. It "is" a healing path. Don't let the limitations you feel, shut you down. Relax, open up, and really focus on the blockage you are experiencing. I find that similar blockages in myself, respond very well to this, I come out whole , on the other side of a cycle where my work, or a few less desirable habits, effect my health. This is relative to my age, too. As I get older, I have to live a better lifestyle to stay healthy. I have also found that qigong gets to deeper and deeper levels of healing. I find new things to work on, that I wasn't aware of before. Sometimes these things rise to the surface and get in your face. It is a often an opportunity to move to the next level.